NPG library
Below is a selection of Reviews, Perspectives, Research Articles and News and Views published by Nature Publishing group journals on the topic of systems biology.
Reviews
Standards for systems biology
Alvis Brazma, Maria Krestyaninova and Ugis Sarkans
doi:10.1038/nrg1922
Nature Reviews Genetics 7, 593-605 (2006)
EGF–ERBB signalling: towards the systems level
Ami Citri and Yosef Yarden
doi:10.1038/nrm1962
Nature Reviews Molecular Cell Biology 7, 505-516 (2006)
Interpreting the protein language using proteomics
Ole N. Jensen
doi:10.1038/nrm1939
Nature Reviews Molecular Cell Biology 7, 391-403 (2006)
Synthetic biology: new engineering rules for an emerging discipline
Ernesto Andrianantoandro, Subhayu Basu, David K Karig and Ron Weiss
doi:10.1038/msb4100073
Molecular Systems Biology 2, published online: 16 May 2006
A comprehensive map of the toll-like receptor signaling network
Kanae Oda and Hiroaki Kitano
doi:10.1038/msb4100057
Molecular Systems Biology 2, published online: 18 April 2006
Modeling cellular machinery through biological network comparison
Roded Sharan and Trey Ideker
doi:10.1038/nbt1196
Nature Biotechnology 24, 427-433 (2006)
Cell-signalling dynamics in time and space
Boris N. Kholodenko
doi:10.1038/nrm1838
Nature Reviews Molecular Cell Biology 7, 165-176 (2006)
Structural systems biology: modelling protein interactions
Patrick Aloy and Robert B. Russell
doi:10.1038/nrm1859
Nature Reviews Molecular Cell Biology 7, 188-197 (2006)
The model organism as a system: integrating 'omics' data sets
Andrew R. Joyce and Bernhard Ø. Palsson
doi:10.1038/nrm1857
Nature Reviews Molecular Cell Biology 7, 198-210 (2006)
Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics
Donald S. Kirkpatrick, Carilee Denison and Steven P. Gygi
doi:10.1038/ncb0805-750
Nature Cell Biology 7, 750-757 (2005)
Perspectives
Systems biology and combination therapy in the quest for clinical efficacy
Jonathan B Fitzgerald, Birgit Schoeberl, Ulrik B Nielsen and Peter K Sorger
doi:10.1038/nchembio817
Nature Chemical Biology 2, 458-466 (2006)
High-throughput fluorescence microscopy for systems biology
Rainer Pepperkok and Jan Ellenberg
doi:10.1038/nrm1979
Nature Reviews Molecular Cell Biology 7, 690-696 (2006)
Proteome chips for whole-organism assays
Li A. Kung and Michael Snyder
doi:10.1038/nrm1941
Nature Reviews Molecular Cell Biology 7, 617-622 (2006)
Research Articles
Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays
Meghana M Kulkarni, Matthew Booker, Serena J Silver, Adam Friedman, Pengyu Hong, Norbert Perrimon and Bernard Mathey-Prevot
doi:10.1038/nmeth935
Nature Methods 3, 833-838 (2006)
State-based discovery: a multidimensional screen for small-molecule modulators of EGF signaling
Mark Sevecka and Gavin MacBeath
doi:10.1038/nmeth931
Nature Methods 3, 825-831 (2006)
Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways
Ben Lehner, Catriona Crombie, Julia Tischler, Angelo Fortunato and Andrew G Fraser
doi:10.1038/ng1844
Nature Genetics 38, 896-903 (2006)
Exploring the regulation of human neural precursor cell differentiation using arrays of signaling microenvironments
Yoav Soen, Akiko Mori, Theo D Palmer and Patrick O Brown
doi:10.1038/msb4100076
Molecular Systems Biology 2, published online: 4 July 2006
ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe
Akihisa Matsuyama, Ritsuko Arai, Yoko Yashiroda, Atsuko Shirai, Ayako Kamata, Shigeko Sekido, Yumiko Kobayashi, Atsushi Hashimoto, Makiko Hamamoto, Yasushi Hiraoka, Sueharu Horinouchi and Minoru Yoshida
doi:10.1038/nbt1222
Nature Biotechnology 24, 841-847 (2006)
Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins
Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Inbal Alaluf, Naamah Swerdlin, Natalie Perzov, Tamar Danon, Yuvalal Liron, Tal Raveh, Anne E Carpenter, Galit Lahav and Uri Alon
doi:10.1038/nmeth892
Nature Methods 3, 525-531 (2006)
Identifying off-target effects and hidden phenotypes of drugs in human cells
Marnie L MacDonald, Jane Lamerdin, Stephen Owens, Brigitte H Keon, Graham K Bilter, Zhidi Shang, Zhengping Huang, Helen Yu, Jennifer Dias, Tomoe Minami, Stephen W Michnick and John K Westwick
doi:10.1038/nchembio790
Nature Chemical Biology 2, 329-337 (2006)
Deciphering principles of transcription regulation in eukaryotic genomes
Dat H Nguyen and Patrik D'haeseleer
doi:10.1038/msb4100054
Molecular Systems Biology 2, published online: 18 April 2006
Functional classification of drugs by properties of their pairwise interactions
Pamela Yeh, Ariane I Tschumi and Roy Kishony
doi:10.1038/ng1755
Nature Genetics 38, 489-494 (2006)
Genetic regulators of large-scale transcriptional signatures in cancer
Adam S Adler, Meihong Lin, Hugo Horlings, Dimitry S A Nuyten, Marc J van de Vijver and Howard Y Chang
doi:10.1038/ng1752
Nature Genetics 38, 421-430 (2006)
High-throughput RNAi screening by time-lapse imaging of live human cells
Beate Neumann, Michael Held, Urban Liebel, Holger Erfle, Phill Rogers, Rainer Pepperkok and Jan Ellenberg
doi:10.1038/nmeth876
Nature Methods 3, 385-390 (2006)
A pooling-deconvolution strategy for biological network elucidation
Fulai Jin, Tony Hazbun, Gregory A Michaud, Michael Salcius, Paul F Predki, Stanley Fields and Jing Huang
doi:10.1038/nmeth859
Nature Methods 3, 183-189 (2006)
Microarrays of lentiviruses for gene function screens in immortalized and primary cells
Steve N Bailey, Siraj M Ali, Anne E Carpenter, Caitlin O Higgins and David M Sabatini
doi:10.1038/nmeth848
Nature Methods 3, 117-122 (2006)
Systems-level analyses identify extensive coupling among gene expression machines
Karolina Maciag, Steven J Altschuler, Michael D Slack, Nevan J Krogan, Andrew Emili, Jack F Greenblatt, Tom Maniatis and Lani F Wu
doi:10.1038/msb4100045
Molecular Systems Biology 2, published online: 17 January 2006
Centering of a radial microtubule array by translocation along microtubules spontaneously nucleated in the cytoplasm
Viacheslav Malikov, Eric N. Cytrynbaum, Anna Kashina, Alexander Mogilner and Vladimir Rodionov
doi:10.1038/ncb1332
Nature Cell Biology 7, 1213-1218 (2005)
Load-dependent kinetics of myosin-V can explain its high processivity
Claudia Veigel, Stephan Schmitz, Fei Wang and James R. Sellers
doi:10.1038/ncb1287
Nature Cell Biology 7, 861-869 (2005)
Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance
Jeffrey P. MacKeigan, Leon O. Murphy and John Blenis
doi:10.1038/ncb1258
Nature Cell Biology 7, 591-600 (2005)
Systematic interpretation of genetic interactions using protein networks
Ryan Kelley and Trey Ideker
doi:10.1038/nbt1096
Nature Biotechnology 23, 561-566 (2005)
Prediction and validation of the distinct dynamics of transient and sustained ERK activation
Satoru Sasagawa, Yu-ichi Ozaki, Kazuhiro Fujita and Shinya Kuroda
doi:10.1038/ncb1233
Nature Cell Biology 7, 365-373 (2005)
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks
Diego di Bernardo, Michael J Thompson, Timothy S Gardner, Sarah E Chobot, Erin L Eastwood, Andrew P Wojtovich, Sean J Elliott, Scott E Schaus and James J Collins
doi:10.1038/nbt1075
Nature Biotechnology 23, 377-383 (2005)
Functional annotation and network reconstruction through cross-platform integration of microarray data
Xianghong Jasmine Zhou, Ming-Chih J Kao, Haiyan Huang, Angela Wong, Juan Nunez-Iglesias, Michael Primig, Oscar M Aparicio, Caleb E Finch, Todd E Morgan and Wing Hung Wong
doi:10.1038/nbt1058
Nature Biotechnology 23, 238-243 (2005)
Mapping the dynamic organization of the nuclear pore complex inside single living cells
Gwénaël Rabut, Valérie Doye and Jan Ellenberg
doi:10.1038/ncb1184
Nature Cell Biology 6, 1114-1121 (2004)
A physical and functional map of the human TNF-
/NF-
B signal transduction pathway
Tewis Bouwmeester, Angela Bauch, Heinz Ruffner, Pierre-Olivier Angrand, Giovanna Bergamini, Karen Croughton, Cristina Cruciat, Dirk Eberhard, Julien Gagneur, Sonja Ghidelli, Carsten Hopf, Bettina Huhse, Raffaella Mangano, Anne-Marie Michon, Markus Schirle, Judith Schlegl, Markus Schwab, Martin A. Stein, Andreas Bauer, Georg Casari, Gerard Drewes, Anne-Claude Gavin, David B. Jackson, Gerard Joberty, Gitte Neubauer, Jens Rick, Bernhard Kuster and Giulio Superti-Furga
doi:10.1038/ncb1086
Nature Cell Biology 6, 97-105 (2004)
Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2
Joseph R. Pomerening, Eduardo D. Sontag and James E. Ferrell, Jr
doi:10.1038/ncb954
Nature Cell Biology 5, 346-351 (2003)
EGFR activation coupled to inhibition of tyrosine phosphatases causes lateral signal propagation
Andrew R. Reynolds, Christian Tischer, Peter J. Verveer, Oliver Rocks and Philippe I. H. Bastiaens
doi:10.1038/ncb981
Nature Cell Biology 5, 447-453 (2003)
News and Views
No strain, no gain
Kathleen M. Trybus
doi:10.1038/ncb0905-854
Nature Cell Biology 7, 854-856 (2005)
Directing NGF's actions: it's a Rap
Philip J. S. Stork
doi:10.1038/ncb0405-338
Nature Cell Biology 7, 338-339 (2005)
Keeping cartographers busy
Matthew S. Hayden and Sankar Ghosh
doi:10.1038/ncb0204-87
Nature Cell Biology 6, 87-89 (2004)
